Iterative pass optimization of sequence data

Cladistics

Volumn 19, Issue 3, 2003, Pages 254-260

  Wheeler, Ward C ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; OPTIMIZATION;

ARTHROPODA;

ALGORITHM; ANIMAL; ARTHROPOD; ARTICLE; CLASSIFICATION; EVOLUTION; GENETICS; METHODOLOGY; MOLECULAR GENETICS; NASA DISCIPLINE EVOLUTIONARY BIOLOGY; NON-NASA CENTER; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

NASA DISCIPLINE EVOLUTIONARY BIOLOGY; NON-NASA CENTER;

ALGORITHMS; ANIMALS; ARTHROPODS; EVOLUTION; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

EID: 0042710797     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2003.tb00368.x     Document Type: Article

References (15)

1. Giribet, G., Wheeler, W.C., Muona, J., 2002. DNA multiple sequence alignments. In: Desalle, R., Giribet, G., Wheeler, W. (Eds.), Molecular Systematics and Evolution: Theory and Practice. Birkhäuser, Basel, pp. 107-114.
2. Giribet, G., Edgecombe, G.D., Wheeler, W.C., 2001. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413, 157-161.
3. Gladstein, D.S., 1997. Efficient incremental character optimization. Cladistics 13, 21-26.
4. Hudson, S.E., 1991. Incremental attribute evaluation: a flexible method for lazy update. ACM Trans. Program. Lang. Syst. 13, 315-341.
5. Needleman, S.B., Wunsch, C.D., 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
6. Sankoff, D., Blanchette, M., 1997. The median problem for breakpoints in comparative genomics. Computing and Combinatorics, 3rd Ann. Int. Conf. COCOON 97 1276, 251-263.
7. Sankoff, D.D., Cedergren, R.J., 1973. A test for nucleotide-sequence homology. J. Mol. Biol. 77, 159-164.
8. Sankoff, D.D., Rousseau, P., 1975. Locating the vertices of a Steiner tree in arbitrary space. Math. Progam. 9, 240-246.
9. Sankoff, D., Cedergren, R.J., Lapalme, G., 1976. Frequency of insertion-deletion, transversion, and transition in the evolutions of 5S ribosomal RNA. J. Mol. Evol. 7, 133-139.
10. Ukkonen, E., 1985. Finding approximate patterns in strings. J. Algorithms 6, 132-137.
11. Wang, L., Jiang, T., 1994. On the complexity of multiple sequence alignment. J. Comput. Biol. 1, 337-348.
12. Wheeler, W.C., 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12, 1-9.
13. Wheeler, W.C., 2002. Optimization alignment: down, up, error, and improvements. In: Desalle, R., Giribet, G., Wheeler, W. (Eds.), Techniques in Molecular Systematics and Evolution. Birkhäuser, Basel, pp. 55-69.
14. Wheeler, W.C., Implied alignment: a synapomorphy-based multiple sequence alignment method and its use in cladogram search. Cladistics, in press.
15. Wheeler, W.C., Gladstein, D.S., Laet, J.D., 2002. POY. Version 3.0. ftp.amnh.org/pub/molecular/poy. Documentation by Daniel Janies and Ward Wheeler.